Multiple sequence alignment - TraesCS4A01G227200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G227200 chr4A 100.000 5717 0 0 1 5717 535432632 535426916 0.000000e+00 10558
1 TraesCS4A01G227200 chr4B 96.640 5685 153 19 1 5662 90499709 90505378 0.000000e+00 9406
2 TraesCS4A01G227200 chr4D 97.451 3178 67 8 1 3166 62103309 62100134 0.000000e+00 5408
3 TraesCS4A01G227200 chr4D 95.585 2514 89 11 3165 5662 62100040 62097533 0.000000e+00 4008
4 TraesCS4A01G227200 chr3D 76.147 327 72 6 1979 2302 103358795 103358472 3.540000e-37 167
5 TraesCS4A01G227200 chr3B 76.147 327 72 6 1979 2302 153962355 153962032 3.540000e-37 167


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G227200 chr4A 535426916 535432632 5716 True 10558 10558 100.000 1 5717 1 chr4A.!!$R1 5716
1 TraesCS4A01G227200 chr4B 90499709 90505378 5669 False 9406 9406 96.640 1 5662 1 chr4B.!!$F1 5661
2 TraesCS4A01G227200 chr4D 62097533 62103309 5776 True 4708 5408 96.518 1 5662 2 chr4D.!!$R1 5661

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
319 320 0.041535 TGGATTGCTGGCATCCCTTT 59.958 50.000 15.78 0.00 33.65 3.11 F
1199 1213 1.171308 CCTGAAGTTGCTGGTGATGG 58.829 55.000 0.00 0.00 0.00 3.51 F
1472 1486 1.377725 CCCCACTGCGAGCTGATTT 60.378 57.895 8.91 0.00 0.00 2.17 F
2676 2697 1.296715 GCTGGTTCCTGGTCATCGT 59.703 57.895 0.00 0.00 0.00 3.73 F
4261 4382 1.362224 AGCCCAGTGATACTGTTGGT 58.638 50.000 8.04 2.33 44.50 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 2299 0.622136 TCAGTTCTGCCTGGCATGAT 59.378 50.000 23.64 5.91 38.13 2.45 R
2509 2530 0.461870 TGCACCGCTTATACTGGCAG 60.462 55.000 14.16 14.16 0.00 4.85 R
3469 3588 3.418995 ACAAAGCATCTCAACTGCATCT 58.581 40.909 0.00 0.00 42.15 2.90 R
4611 4735 0.533032 GAGTAGCCAGTGGACCAGAC 59.467 60.000 15.20 2.27 0.00 3.51 R
5678 5819 0.094558 GCGACGTTGCAATCGATCAA 59.905 50.000 22.96 0.00 40.86 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 0.995024 AGGTGGGGGAGATTGTTCAG 59.005 55.000 0.00 0.00 0.00 3.02
140 141 3.437741 GCCATTGCATTTTCTTGAAAGGG 59.562 43.478 0.00 0.00 38.81 3.95
171 172 5.010282 GCGGGAAATTAAGGTATCCATCAT 58.990 41.667 0.00 0.00 33.48 2.45
280 281 8.723942 AGAGCCTAAATTGATTAGTTGTGTAG 57.276 34.615 0.00 0.00 39.56 2.74
307 308 7.092716 ACAAGATTGTAGTTTTCATGGATTGC 58.907 34.615 0.00 0.00 40.16 3.56
319 320 0.041535 TGGATTGCTGGCATCCCTTT 59.958 50.000 15.78 0.00 33.65 3.11
468 469 6.070021 ACCAGAAGAATGACCAGTTCATGATA 60.070 38.462 0.00 0.00 44.86 2.15
684 695 4.559153 AGCTTCAAAATGTGGAATTTCGG 58.441 39.130 0.00 0.00 0.00 4.30
767 778 7.934855 AGAGTTAGAAATTGCAATCATGACT 57.065 32.000 13.38 12.94 0.00 3.41
773 784 6.802608 AGAAATTGCAATCATGACTATGGTG 58.197 36.000 13.38 0.00 34.97 4.17
877 889 6.321181 ACTTTGCACTCAAGTTGAAGGAAATA 59.679 34.615 18.45 5.03 33.12 1.40
957 971 8.811378 GTCAAATTAAAATATCTTCAAGGCTGC 58.189 33.333 0.00 0.00 0.00 5.25
989 1003 2.555757 AGAAGTTCAGGCATTGCTTGTC 59.444 45.455 18.83 13.44 36.96 3.18
1199 1213 1.171308 CCTGAAGTTGCTGGTGATGG 58.829 55.000 0.00 0.00 0.00 3.51
1248 1262 4.578105 CAGTTGAAAGAGAAGCCAGTTCTT 59.422 41.667 0.00 0.00 46.21 2.52
1334 1348 4.023279 GCACAATGGCATAATTGGACGATA 60.023 41.667 0.00 0.00 41.06 2.92
1472 1486 1.377725 CCCCACTGCGAGCTGATTT 60.378 57.895 8.91 0.00 0.00 2.17
1683 1704 1.596727 GCCAAAATTGTTGCGCTCAAA 59.403 42.857 18.62 7.09 33.37 2.69
1697 1718 1.858458 GCTCAAAAAGGTTCGGTTTGC 59.142 47.619 0.00 0.00 33.26 3.68
1792 1813 9.196139 CCAATGTTATAAAGTTGGAAGGGATAA 57.804 33.333 18.66 0.00 42.88 1.75
1989 2010 2.564947 GAGTCTCATCCAGGTCAAGTGT 59.435 50.000 0.00 0.00 0.00 3.55
2005 2026 6.349611 GGTCAAGTGTTTGATGCAACAGATAT 60.350 38.462 0.00 0.00 44.62 1.63
2118 2139 2.276732 TTGCTGACTTTGGCTTAGCT 57.723 45.000 3.59 0.00 35.50 3.32
2266 2287 2.086094 GCATTTTTGGGGAATTGCTGG 58.914 47.619 0.00 0.00 34.65 4.85
2533 2554 1.942657 CAGTATAAGCGGTGCATTGCT 59.057 47.619 10.49 9.59 44.97 3.91
2623 2644 2.031012 CGTGGAACAGCTGCCTCA 59.969 61.111 15.27 6.50 41.80 3.86
2676 2697 1.296715 GCTGGTTCCTGGTCATCGT 59.703 57.895 0.00 0.00 0.00 3.73
2867 2889 8.552083 ACTTTTAGGTTACCACGGTATAAAAG 57.448 34.615 23.63 23.63 41.08 2.27
2975 2998 8.689061 ACAACTTTCATGCATATGTTATGTCAT 58.311 29.630 16.51 4.39 35.73 3.06
3055 3078 6.053632 TGAAGCATTTGGACTAGATCTGAA 57.946 37.500 5.18 0.00 0.00 3.02
3062 3085 5.407407 TTGGACTAGATCTGAACTTGGTC 57.593 43.478 5.18 10.14 0.00 4.02
3070 3093 5.684704 AGATCTGAACTTGGTCAGTTTTCA 58.315 37.500 14.40 0.00 46.53 2.69
3084 3107 4.766373 TCAGTTTTCAGCTTATTGCATGGA 59.234 37.500 0.00 0.00 45.94 3.41
3098 3122 4.532314 TGCATGGAAAATTGTGCATACA 57.468 36.364 1.82 0.36 42.13 2.29
3469 3588 6.448369 TCCTTTCTTTCTGTTCATAGGGAA 57.552 37.500 0.00 0.00 0.00 3.97
3507 3626 6.065374 TGCTTTGTTAGTTGACCCAGAAATA 58.935 36.000 0.00 0.00 0.00 1.40
3521 3640 5.474876 ACCCAGAAATACTTCTTGCTCTTTG 59.525 40.000 0.00 0.00 40.05 2.77
3580 3699 6.258947 GGAATTGAGAATCCTAGAGAAAACCG 59.741 42.308 0.00 0.00 32.75 4.44
3684 3803 6.335471 AGTTTTTCATTGATGATCACTGCA 57.665 33.333 7.80 0.00 36.56 4.41
3974 4095 3.676646 ACGAAGTACCTGAACGCAAATAC 59.323 43.478 0.00 0.00 41.94 1.89
3976 4097 4.201589 CGAAGTACCTGAACGCAAATACAG 60.202 45.833 0.00 0.00 0.00 2.74
4062 4183 1.369625 GACTGGCGTAGGGAACATTG 58.630 55.000 0.00 0.00 0.00 2.82
4088 4209 5.240891 CCTGCTTCTCACAACAAAGAGATA 58.759 41.667 0.00 0.00 40.32 1.98
4137 4258 8.608844 AAGTATGGTAATGCTAAAGATAGTGC 57.391 34.615 0.00 0.00 0.00 4.40
4213 4334 7.590322 CAGCAGAAAATCACATAATATGTCAGC 59.410 37.037 2.41 0.52 42.70 4.26
4219 4340 6.957984 ATCACATAATATGTCAGCTAAGCG 57.042 37.500 2.41 0.00 42.70 4.68
4261 4382 1.362224 AGCCCAGTGATACTGTTGGT 58.638 50.000 8.04 2.33 44.50 3.67
4507 4630 6.834451 TGGTTTCTTTTGTATGTACCTTCCAA 59.166 34.615 0.00 0.00 0.00 3.53
4546 4669 8.974060 AACATTTTGAGTGTCTCTTACCTAAA 57.026 30.769 0.00 0.00 0.00 1.85
4611 4735 7.830739 AGGGTAAGAGCAAAATAGTCAATTTG 58.169 34.615 0.00 0.00 37.85 2.32
4621 4745 6.575162 AAATAGTCAATTTGTCTGGTCCAC 57.425 37.500 6.44 0.00 36.41 4.02
4844 4968 2.163211 GAGCAACTTCTCTCCAAATGGC 59.837 50.000 0.00 0.00 34.44 4.40
4917 5041 0.810031 CAAGAGTTGGGCGATACCGG 60.810 60.000 0.00 0.00 40.62 5.28
4934 5058 7.041848 GCGATACCGGTACCATTATTTTTAAGT 60.042 37.037 18.55 0.00 36.06 2.24
5021 5145 0.257039 ATGGTGAAGCTTAGGGGCTG 59.743 55.000 0.00 0.00 42.24 4.85
5022 5146 1.077429 GGTGAAGCTTAGGGGCTGG 60.077 63.158 0.00 0.00 42.24 4.85
5072 5201 2.879646 TGTAGCGGATTTTTGACGGTTT 59.120 40.909 0.00 0.00 39.24 3.27
5077 5206 3.175929 CGGATTTTTGACGGTTTATGGC 58.824 45.455 0.00 0.00 0.00 4.40
5267 5401 3.066208 AGTCCAGTATCCCACCATGAT 57.934 47.619 0.00 0.00 0.00 2.45
5338 5472 3.965539 CTTGGGCCTGCCTCAGTCG 62.966 68.421 4.53 0.00 36.10 4.18
5381 5515 4.553323 ACATGAAAATGCAGAAGCTGAAC 58.447 39.130 0.00 0.00 42.74 3.18
5467 5601 9.558396 TGAAAAATTAGGAAAAATGCAATGACT 57.442 25.926 0.00 0.00 0.00 3.41
5477 5611 6.690194 AAAATGCAATGACTAGATCAGACC 57.310 37.500 0.00 0.00 41.91 3.85
5506 5646 5.100811 TCCTATGACATATACCCCATTGCT 58.899 41.667 0.00 0.00 0.00 3.91
5518 5658 2.487934 CCCATTGCTCCGTATCTTGAG 58.512 52.381 0.00 0.00 0.00 3.02
5536 5676 5.946972 TCTTGAGAACAAAAGGTGGTTGTAA 59.053 36.000 0.00 0.00 38.24 2.41
5580 5720 3.921021 GTGGTTAGTTCATGAGTCGACTG 59.079 47.826 25.58 10.12 0.00 3.51
5662 5803 1.306141 TGACTCCCTACCTGGCTGG 60.306 63.158 9.11 9.11 42.93 4.85
5663 5804 2.041265 ACTCCCTACCTGGCTGGG 59.959 66.667 15.36 16.04 42.20 4.45
5664 5805 2.041265 CTCCCTACCTGGCTGGGT 59.959 66.667 19.88 11.21 41.58 4.51
5665 5806 2.285368 TCCCTACCTGGCTGGGTG 60.285 66.667 19.88 6.65 41.58 4.61
5666 5807 3.411517 CCCTACCTGGCTGGGTGG 61.412 72.222 15.36 14.62 40.22 4.61
5667 5808 4.115199 CCTACCTGGCTGGGTGGC 62.115 72.222 15.36 0.00 40.22 5.01
5669 5810 3.628646 CTACCTGGCTGGGTGGCAC 62.629 68.421 15.36 9.70 46.76 5.01
5671 5812 2.757145 TACCTGGCTGGGTGGCACTA 62.757 60.000 18.45 6.28 46.76 2.74
5672 5813 2.045926 CTGGCTGGGTGGCACTAC 60.046 66.667 18.45 11.49 46.76 2.73
5673 5814 2.851588 TGGCTGGGTGGCACTACA 60.852 61.111 18.45 15.43 46.76 2.74
5674 5815 2.202236 CTGGCTGGGTGGCACTACAT 62.202 60.000 18.45 0.00 46.76 2.29
5675 5816 1.000896 GGCTGGGTGGCACTACATT 60.001 57.895 18.45 0.00 41.37 2.71
5676 5817 1.315257 GGCTGGGTGGCACTACATTG 61.315 60.000 18.45 7.52 41.37 2.82
5677 5818 1.937546 GCTGGGTGGCACTACATTGC 61.938 60.000 18.45 13.08 42.18 3.56
5678 5819 0.322816 CTGGGTGGCACTACATTGCT 60.323 55.000 18.45 0.00 42.56 3.91
5679 5820 0.112218 TGGGTGGCACTACATTGCTT 59.888 50.000 18.45 0.00 42.56 3.91
5680 5821 0.527565 GGGTGGCACTACATTGCTTG 59.472 55.000 18.45 0.00 42.56 4.01
5681 5822 1.533625 GGTGGCACTACATTGCTTGA 58.466 50.000 18.45 0.00 42.56 3.02
5682 5823 2.094675 GGTGGCACTACATTGCTTGAT 58.905 47.619 18.45 0.00 42.56 2.57
5683 5824 2.098117 GGTGGCACTACATTGCTTGATC 59.902 50.000 18.45 0.00 42.56 2.92
5684 5825 2.009051 TGGCACTACATTGCTTGATCG 58.991 47.619 0.00 0.00 42.56 3.69
5685 5826 2.279741 GGCACTACATTGCTTGATCGA 58.720 47.619 0.00 0.00 42.56 3.59
5686 5827 2.874701 GGCACTACATTGCTTGATCGAT 59.125 45.455 0.00 0.00 42.56 3.59
5687 5828 3.313526 GGCACTACATTGCTTGATCGATT 59.686 43.478 0.00 0.00 42.56 3.34
5688 5829 4.277258 GCACTACATTGCTTGATCGATTG 58.723 43.478 0.00 0.00 39.59 2.67
5689 5830 4.277258 CACTACATTGCTTGATCGATTGC 58.723 43.478 0.00 5.72 0.00 3.56
5690 5831 3.940852 ACTACATTGCTTGATCGATTGCA 59.059 39.130 14.64 14.64 0.00 4.08
5692 5833 3.504863 ACATTGCTTGATCGATTGCAAC 58.495 40.909 25.43 11.71 46.08 4.17
5693 5834 2.245795 TTGCTTGATCGATTGCAACG 57.754 45.000 21.81 8.22 39.98 4.10
5694 5835 1.155889 TGCTTGATCGATTGCAACGT 58.844 45.000 15.77 8.10 32.12 3.99
5695 5836 1.128507 TGCTTGATCGATTGCAACGTC 59.871 47.619 15.77 14.35 32.12 4.34
5696 5837 1.848186 GCTTGATCGATTGCAACGTCG 60.848 52.381 14.76 14.76 39.11 5.12
5697 5838 0.094558 TTGATCGATTGCAACGTCGC 59.905 50.000 15.84 0.00 37.74 5.19
5698 5839 1.011451 TGATCGATTGCAACGTCGCA 61.011 50.000 15.84 0.00 41.03 5.10
5699 5840 0.301687 GATCGATTGCAACGTCGCAT 59.698 50.000 15.84 10.85 42.62 4.73
5700 5841 0.026674 ATCGATTGCAACGTCGCATG 59.973 50.000 15.84 0.00 42.62 4.06
5701 5842 1.580893 CGATTGCAACGTCGCATGG 60.581 57.895 0.04 0.00 42.62 3.66
5702 5843 1.793581 GATTGCAACGTCGCATGGA 59.206 52.632 0.04 0.00 42.62 3.41
5703 5844 0.167908 GATTGCAACGTCGCATGGAA 59.832 50.000 0.04 0.00 42.62 3.53
5704 5845 0.595588 ATTGCAACGTCGCATGGAAA 59.404 45.000 0.04 0.00 42.62 3.13
5705 5846 0.382158 TTGCAACGTCGCATGGAAAA 59.618 45.000 0.04 0.00 42.62 2.29
5706 5847 0.595588 TGCAACGTCGCATGGAAAAT 59.404 45.000 0.00 0.00 36.86 1.82
5707 5848 1.000827 TGCAACGTCGCATGGAAAATT 60.001 42.857 0.00 0.00 36.86 1.82
5708 5849 2.058057 GCAACGTCGCATGGAAAATTT 58.942 42.857 0.00 0.00 0.00 1.82
5709 5850 3.238441 GCAACGTCGCATGGAAAATTTA 58.762 40.909 0.00 0.00 0.00 1.40
5710 5851 3.670991 GCAACGTCGCATGGAAAATTTAA 59.329 39.130 0.00 0.00 0.00 1.52
5711 5852 4.149046 GCAACGTCGCATGGAAAATTTAAA 59.851 37.500 0.00 0.00 0.00 1.52
5712 5853 5.332656 GCAACGTCGCATGGAAAATTTAAAA 60.333 36.000 0.00 0.00 0.00 1.52
5713 5854 6.617529 GCAACGTCGCATGGAAAATTTAAAAT 60.618 34.615 0.00 0.00 0.00 1.82
5714 5855 6.388259 ACGTCGCATGGAAAATTTAAAATG 57.612 33.333 0.00 0.00 0.00 2.32
5715 5856 5.923684 ACGTCGCATGGAAAATTTAAAATGT 59.076 32.000 0.00 0.00 0.00 2.71
5716 5857 7.085116 ACGTCGCATGGAAAATTTAAAATGTA 58.915 30.769 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 0.806241 TTAATTTCCCGCTTGACGCC 59.194 50.000 0.00 0.00 41.76 5.68
280 281 6.817765 TCCATGAAAACTACAATCTTGTCC 57.182 37.500 0.00 0.00 42.35 4.02
307 308 2.426024 CAACATGAGAAAGGGATGCCAG 59.574 50.000 5.86 0.00 0.00 4.85
319 320 7.552687 ACAAGTTAAGAAGTCAACAACATGAGA 59.447 33.333 0.00 0.00 0.00 3.27
468 469 6.666678 TCAAAATTCCATCTTCTGAGGCTAT 58.333 36.000 0.00 0.00 0.00 2.97
562 563 7.148239 ACCAAAGTCACAAGTTAAGAAGTCAAG 60.148 37.037 0.00 0.00 0.00 3.02
684 695 2.554032 ACTGTAAGCAGCCAAATGTGAC 59.446 45.455 0.00 0.00 46.30 3.67
957 971 4.756642 TGCCTGAACTTCTCAATGTTACAG 59.243 41.667 0.00 0.00 32.17 2.74
1199 1213 2.436417 TGGGCACTTCTGTATTTCTGC 58.564 47.619 0.00 0.00 0.00 4.26
1334 1348 8.105197 AGAAACCTAAATCCAGTTTATTACCGT 58.895 33.333 0.00 0.00 34.00 4.83
1683 1704 2.959707 TGTATTGGCAAACCGAACCTTT 59.040 40.909 3.01 0.00 39.70 3.11
1697 1718 4.095483 GCACACTTTCAGGATCTGTATTGG 59.905 45.833 0.00 0.00 32.61 3.16
1989 2010 6.405731 GGCCACTAAATATCTGTTGCATCAAA 60.406 38.462 0.00 0.00 0.00 2.69
2005 2026 2.760092 GGCAATGATCAAGGCCACTAAA 59.240 45.455 27.16 0.00 45.70 1.85
2118 2139 6.738731 GCCGACTCTCAGGATCATAAAATGTA 60.739 42.308 0.00 0.00 0.00 2.29
2266 2287 1.520787 GCATGATTGGCTTGGCAGC 60.521 57.895 0.00 1.00 46.52 5.25
2278 2299 0.622136 TCAGTTCTGCCTGGCATGAT 59.378 50.000 23.64 5.91 38.13 2.45
2397 2418 3.492102 GCTCCACCTAGCATGGAATTA 57.508 47.619 13.36 0.00 45.67 1.40
2509 2530 0.461870 TGCACCGCTTATACTGGCAG 60.462 55.000 14.16 14.16 0.00 4.85
2533 2554 8.884124 ATGGAGGTAAATCTTTGAAATTCTCA 57.116 30.769 0.00 0.00 0.00 3.27
2623 2644 5.517322 AACTTACGTCACTCTGAAGACTT 57.483 39.130 0.00 0.00 32.68 3.01
2947 2970 8.692110 ACATAACATATGCATGAAAGTTGTTG 57.308 30.769 19.56 11.99 35.96 3.33
3055 3078 5.507985 GCAATAAGCTGAAAACTGACCAAGT 60.508 40.000 0.00 0.00 39.96 3.16
3062 3085 5.063180 TCCATGCAATAAGCTGAAAACTG 57.937 39.130 0.00 0.00 45.94 3.16
3070 3093 4.632688 GCACAATTTTCCATGCAATAAGCT 59.367 37.500 0.00 0.00 45.94 3.74
3084 3107 4.870123 TTCAGGCTGTATGCACAATTTT 57.130 36.364 15.27 0.00 45.15 1.82
3098 3122 7.059156 ACAAAATCTGATAGCTTATTCAGGCT 58.941 34.615 16.45 0.00 41.92 4.58
3296 3415 6.367969 GGATACATAGGTTAAATGCTGGTACG 59.632 42.308 0.00 0.00 0.00 3.67
3469 3588 3.418995 ACAAAGCATCTCAACTGCATCT 58.581 40.909 0.00 0.00 42.15 2.90
3507 3626 5.489792 TGTCTATCCAAAGAGCAAGAAGT 57.510 39.130 0.00 0.00 0.00 3.01
3521 3640 3.914426 TCTGGCCTTCTTTGTCTATCC 57.086 47.619 3.32 0.00 0.00 2.59
3537 3656 3.808466 TCCTGATCGAACAGATTCTGG 57.192 47.619 22.88 11.88 40.26 3.86
3580 3699 6.438763 GGTTTAATAGAACCATATGCAGCAC 58.561 40.000 0.00 0.00 46.66 4.40
3620 3739 1.135717 TCAACAAATGATTGCCGAGCG 60.136 47.619 0.00 0.00 40.34 5.03
3684 3803 3.690460 AGGCATTCCGTTTCTTCTGATT 58.310 40.909 0.00 0.00 37.47 2.57
3926 4047 6.833346 TGGTCCATATAATTGTTACCTCCA 57.167 37.500 0.00 0.00 0.00 3.86
4062 4183 1.024271 TTGTTGTGAGAAGCAGGCAC 58.976 50.000 0.00 0.00 0.00 5.01
4088 4209 1.716503 ACCATTGGGCCTTTTACTCCT 59.283 47.619 4.53 0.00 37.90 3.69
4213 4334 2.365408 AAAGGTCCTCGAACGCTTAG 57.635 50.000 0.00 0.00 0.00 2.18
4261 4382 2.097304 CAGCATAAACAGCGCCAATACA 59.903 45.455 2.29 0.00 37.01 2.29
4611 4735 0.533032 GAGTAGCCAGTGGACCAGAC 59.467 60.000 15.20 2.27 0.00 3.51
4621 4745 2.237143 TGTTCCCATCTTGAGTAGCCAG 59.763 50.000 0.00 0.00 0.00 4.85
4864 4988 3.191371 AGCTGTACAAAAATGGCAGTAGC 59.809 43.478 0.00 0.00 41.10 3.58
4917 5041 8.276252 TCTGCCTCACTTAAAAATAATGGTAC 57.724 34.615 0.00 0.00 0.00 3.34
5021 5145 4.452825 GCTTGTATTTCTTAGACCTCCCC 58.547 47.826 0.00 0.00 0.00 4.81
5022 5146 4.080526 TGGCTTGTATTTCTTAGACCTCCC 60.081 45.833 0.00 0.00 0.00 4.30
5072 5201 5.063204 CGAAGACAAAATATGAGGGCCATA 58.937 41.667 6.18 0.00 41.58 2.74
5077 5206 5.817296 TCATCACGAAGACAAAATATGAGGG 59.183 40.000 0.00 0.00 0.00 4.30
5124 5253 5.818678 TTGTACTGTACATCCTTCCTTGT 57.181 39.130 20.31 0.00 38.68 3.16
5267 5401 2.844654 AATGCATCCACCATGGGTTA 57.155 45.000 18.09 0.00 38.32 2.85
5467 5601 7.933223 TGTCATAGGAGATATGGTCTGATCTA 58.067 38.462 0.00 0.00 41.51 1.98
5477 5611 8.733092 ATGGGGTATATGTCATAGGAGATATG 57.267 38.462 15.17 0.00 39.54 1.78
5506 5646 4.994852 CACCTTTTGTTCTCAAGATACGGA 59.005 41.667 0.00 0.00 34.88 4.69
5518 5658 6.801575 TCAGATTTACAACCACCTTTTGTTC 58.198 36.000 0.00 0.00 38.21 3.18
5536 5676 5.416952 CACCTTTTGTTAGCAGGATCAGATT 59.583 40.000 0.00 0.00 0.00 2.40
5580 5720 4.314961 CAACAACTTAAAAGGAATGGCCC 58.685 43.478 0.00 0.00 37.37 5.80
5662 5803 1.533625 TCAAGCAATGTAGTGCCACC 58.466 50.000 0.18 0.00 46.14 4.61
5663 5804 2.223112 CGATCAAGCAATGTAGTGCCAC 60.223 50.000 0.18 0.00 46.14 5.01
5664 5805 2.009051 CGATCAAGCAATGTAGTGCCA 58.991 47.619 0.18 0.00 46.14 4.92
5665 5806 2.279741 TCGATCAAGCAATGTAGTGCC 58.720 47.619 0.18 0.00 46.14 5.01
5666 5807 4.277258 CAATCGATCAAGCAATGTAGTGC 58.723 43.478 0.00 0.00 45.28 4.40
5667 5808 4.201841 TGCAATCGATCAAGCAATGTAGTG 60.202 41.667 15.12 0.06 33.48 2.74
5668 5809 3.940852 TGCAATCGATCAAGCAATGTAGT 59.059 39.130 15.12 0.00 33.48 2.73
5669 5810 4.541085 TGCAATCGATCAAGCAATGTAG 57.459 40.909 15.12 0.00 33.48 2.74
5670 5811 4.961435 TTGCAATCGATCAAGCAATGTA 57.039 36.364 21.55 3.80 41.55 2.29
5671 5812 3.853831 TTGCAATCGATCAAGCAATGT 57.146 38.095 21.55 0.00 41.55 2.71
5674 5815 1.535028 ACGTTGCAATCGATCAAGCAA 59.465 42.857 21.55 21.55 43.90 3.91
5675 5816 1.128507 GACGTTGCAATCGATCAAGCA 59.871 47.619 22.26 13.92 34.79 3.91
5676 5817 1.802839 GACGTTGCAATCGATCAAGC 58.197 50.000 22.26 4.36 0.00 4.01
5677 5818 1.848186 GCGACGTTGCAATCGATCAAG 60.848 52.381 22.96 11.68 40.86 3.02
5678 5819 0.094558 GCGACGTTGCAATCGATCAA 59.905 50.000 22.96 0.00 40.86 2.57
5679 5820 1.011451 TGCGACGTTGCAATCGATCA 61.011 50.000 27.97 11.40 43.02 2.92
5680 5821 1.707451 TGCGACGTTGCAATCGATC 59.293 52.632 27.97 15.61 43.02 3.69
5681 5822 3.869187 TGCGACGTTGCAATCGAT 58.131 50.000 27.97 10.18 43.02 3.59
5688 5829 1.696988 AATTTTCCATGCGACGTTGC 58.303 45.000 21.27 21.27 0.00 4.17
5689 5830 5.814314 TTTAAATTTTCCATGCGACGTTG 57.186 34.783 0.00 0.00 0.00 4.10
5690 5831 6.422400 ACATTTTAAATTTTCCATGCGACGTT 59.578 30.769 0.00 0.00 0.00 3.99
5691 5832 5.923684 ACATTTTAAATTTTCCATGCGACGT 59.076 32.000 0.00 0.00 0.00 4.34
5692 5833 6.388259 ACATTTTAAATTTTCCATGCGACG 57.612 33.333 0.00 0.00 0.00 5.12


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.